src/constraints/Rattle.cpp

 /*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
 
#include "constraints/Rattle.hpp"
#include "primitives/Molecule.hpp"
#include "utils/simError.h"
namespace oopse {

Rattle::Rattle(SimInfo* info) : info_(info), maxConsIteration_(10), consTolerance_(1.0e-6) {
    
    if (info_->getSimParams()->haveDt()) {
        dt_ = info_->getSimParams()->getDt();
    } else {
            sprintf(painCave.errMsg,
                    "Integrator Error: dt is not set\n");
            painCave.isFatal = 1;
            simError();
    }    
    
    currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
}

void Rattle::constraintA() {
    if (info_->getNConstraints() > 0) {
        doConstraint(&Rattle::constraintPairA);
    }
}
void Rattle::constraintB() {
    if (info_->getNConstraints() > 0) {
        doConstraint(&Rattle::constraintPairB);
    }
}

void Rattle::doConstraint(ConstraintPairFuncPtr func) {
    Molecule* mol;
    SimInfo::MoleculeIterator mi;
    ConstraintElem* consElem;
    Molecule::ConstraintElemIterator cei;
    ConstraintPair* consPair;
    Molecule::ConstraintPairIterator cpi;
    
    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
        for (consElem = mol->beginConstraintElem(cei); consElem != NULL; consElem = mol->nextConstraintElem(cei)) {
            consElem->setMoved(true);
            consElem->setMoving(false);
        }
    }
    
    //main loop of constraint algorithm
    bool done = false;
    int iteration = 0;
    while(!done && iteration < maxConsIteration_){
        done = true;

        //loop over every constraint pair

        for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
            for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) {


                //dispatch constraint algorithm
                if(consPair->isMoved()) {
                    int exeStatus = (this->*func)(consPair);

                    switch(exeStatus){
                        case consFail:
                            sprintf(painCave.errMsg,
                            "Constraint failure in Rattle::constrainA, Constraint Fail\n");
                            painCave.isFatal = 1;
                            simError();                             
                            
                            break;
                        case consSuccess:
                            //constrain the pair by moving two elements
                            done = false;
                            consPair->getConsElem1()->setMoving(true);
                            consPair->getConsElem2()->setMoving(true);
                            break;
                        case consAlready:
                            //current pair is already constrained, do not need to move the elements
                            break;
                        default:          
                            sprintf(painCave.errMsg, "ConstraintAlgorithm::doConstrain() Error: unrecognized status");
                            painCave.isFatal = 1;
                            simError();                           
                            break;
                    }      
                }
            }
        }//end for(iter->first())


        for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
            for (consElem = mol->beginConstraintElem(cei); consElem != NULL; consElem = mol->nextConstraintElem(cei)) {
                consElem->setMoved(consElem->getMoving());
                consElem->setMoving(false);
            }
        }

        iteration++;
    }//end while

    if (!done){
      sprintf(painCave.errMsg,
              "Constraint failure in Rattle::constrainA, too many iterations: %d\n",
              iteration);
      painCave.isFatal = 1;
      simError();    
    }
}

int Rattle::constraintPairA(ConstraintPair* consPair){
  ConstraintElem* consElem1 = consPair->getConsElem1();
  ConstraintElem* consElem2 = consPair->getConsElem2();

  Vector3d posA = consElem1->getPos();
  Vector3d posB = consElem2->getPos();

  Vector3d pab = posA -posB;   

  //periodic boundary condition

  currentSnapshot_->wrapVector(pab);

  double pabsq = pab.lengthSquare();

  double rabsq = consPair->getConsDistSquare();
  double diffsq = rabsq - pabsq;

  // the original rattle code from alan tidesley
  if (fabs(diffsq) > (consTolerance_ * rabsq * 2)){
    
    Vector3d oldPosA = consElem1->getPrevPos();
    Vector3d oldPosB = consElem2->getPrevPos();      

    Vector3d rab = oldPosA - oldPosB;    

    currentSnapshot_->wrapVector(rab);

    double rpab = dot(rab, pab);
    double rpabsq = rpab * rpab;

    if (rpabsq < (rabsq * -diffsq)){
      return consFail;
    }

    double rma = 1.0 / consElem1->getMass();
    double rmb = 1.0 / consElem2->getMass();

    double gab = diffsq / (2.0 * (rma + rmb) * rpab);

    Vector3d delta = rab * gab;

    //set atom1's position
    posA += rma * delta;    
    consElem1->setPos(posA);

    //set atom2's position
    posB -= rmb * delta;
    consElem2->setPos(posB);

    delta /= dt_;
    
    //set atom1's velocity
    Vector3d velA = consElem1->getVel();
    velA += rma * delta;
    consElem1->setVel(velA);

    //set atom2's velocity
    Vector3d velB = consElem2->getVel();
    velB -= rmb * delta;
    consElem2->setVel(velB);

    return consSuccess;
  }
  else
    return consAlready;
  
}


int Rattle::constraintPairB(ConstraintPair* consPair){
    ConstraintElem* consElem1 = consPair->getConsElem1();
    ConstraintElem* consElem2 = consPair->getConsElem2();

  
    Vector3d velA = consElem1->getVel();
    Vector3d velB = consElem2->getVel();

    Vector3d dv = velA - velB;

    Vector3d posA = consElem1->getPos();
    Vector3d posB = consElem2->getPos();

    Vector3d rab = posA - posB;

    currentSnapshot_->wrapVector(rab);

    double rma = 1.0 / consElem1->getMass();
    double rmb = 1.0 / consElem2->getMass();

    double rvab = dot(rab, dv);

    double gab = -rvab / ((rma + rmb) * consPair->getConsDistSquare());

    if (fabs(gab) > consTolerance_){
      Vector3d delta = rab * gab;
      
      velA += rma * delta;
      consElem1->setVel(velA);
      
      velB -= rmb * delta;
      consElem2->setVel(velB);

      return consSuccess;
    }
    else
      return consAlready;

}

}
Revision:	1930
Committed:	Wed Jan 12 22:41:40 2005 UTC (20 years, 9 months ago) by gezelter
File size:	8434 byte(s)
Log Message:	merging new_design branch into OOPSE-2.0
#	User	Rev	Content
1	gezelter	1930	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			#include "constraints/Rattle.hpp"
43			#include "primitives/Molecule.hpp"
44			#include "utils/simError.h"
45			namespace oopse {
46
47			Rattle::Rattle(SimInfo* info) : info_(info), maxConsIteration_(10), consTolerance_(1.0e-6) {
48
49			if (info_->getSimParams()->haveDt()) {
50			dt_ = info_->getSimParams()->getDt();
51			} else {
52			sprintf(painCave.errMsg,
53			"Integrator Error: dt is not set\n");
54			painCave.isFatal = 1;
55			simError();
56			}
57
58			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
59			}
60
61			void Rattle::constraintA() {
62			if (info_->getNConstraints() > 0) {
63			doConstraint(&Rattle::constraintPairA);
64			}
65			}
66			void Rattle::constraintB() {
67			if (info_->getNConstraints() > 0) {
68			doConstraint(&Rattle::constraintPairB);
69			}
70			}
71
72			void Rattle::doConstraint(ConstraintPairFuncPtr func) {
73			Molecule* mol;
74			SimInfo::MoleculeIterator mi;
75			ConstraintElem* consElem;
76			Molecule::ConstraintElemIterator cei;
77			ConstraintPair* consPair;
78			Molecule::ConstraintPairIterator cpi;
79
80			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
81			for (consElem = mol->beginConstraintElem(cei); consElem != NULL; consElem = mol->nextConstraintElem(cei)) {
82			consElem->setMoved(true);
83			consElem->setMoving(false);
84			}
85			}
86
87			//main loop of constraint algorithm
88			bool done = false;
89			int iteration = 0;
90			while(!done && iteration < maxConsIteration_){
91			done = true;
92
93			//loop over every constraint pair
94
95			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
96			for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) {
97
98
99			//dispatch constraint algorithm
100			if(consPair->isMoved()) {
101			int exeStatus = (this->*func)(consPair);
102
103			switch(exeStatus){
104			case consFail:
105			sprintf(painCave.errMsg,
106			"Constraint failure in Rattle::constrainA, Constraint Fail\n");
107			painCave.isFatal = 1;
108			simError();
109
110			break;
111			case consSuccess:
112			//constrain the pair by moving two elements
113			done = false;
114			consPair->getConsElem1()->setMoving(true);
115			consPair->getConsElem2()->setMoving(true);
116			break;
117			case consAlready:
118			//current pair is already constrained, do not need to move the elements
119			break;
120			default:
121			sprintf(painCave.errMsg, "ConstraintAlgorithm::doConstrain() Error: unrecognized status");
122			painCave.isFatal = 1;
123			simError();
124			break;
125			}
126			}
127			}
128			}//end for(iter->first())
129
130
131			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
132			for (consElem = mol->beginConstraintElem(cei); consElem != NULL; consElem = mol->nextConstraintElem(cei)) {
133			consElem->setMoved(consElem->getMoving());
134			consElem->setMoving(false);
135			}
136			}
137
138			iteration++;
139			}//end while
140
141			if (!done){
142			sprintf(painCave.errMsg,
143			"Constraint failure in Rattle::constrainA, too many iterations: %d\n",
144			iteration);
145			painCave.isFatal = 1;
146			simError();
147			}
148			}
149
150			int Rattle::constraintPairA(ConstraintPair* consPair){
151			ConstraintElem* consElem1 = consPair->getConsElem1();
152			ConstraintElem* consElem2 = consPair->getConsElem2();
153
154			Vector3d posA = consElem1->getPos();
155			Vector3d posB = consElem2->getPos();
156
157			Vector3d pab = posA -posB;
158
159			//periodic boundary condition
160
161			currentSnapshot_->wrapVector(pab);
162
163			double pabsq = pab.lengthSquare();
164
165			double rabsq = consPair->getConsDistSquare();
166			double diffsq = rabsq - pabsq;
167
168			// the original rattle code from alan tidesley
169			if (fabs(diffsq) > (consTolerance_ * rabsq * 2)){
170
171			Vector3d oldPosA = consElem1->getPrevPos();
172			Vector3d oldPosB = consElem2->getPrevPos();
173
174			Vector3d rab = oldPosA - oldPosB;
175
176			currentSnapshot_->wrapVector(rab);
177
178			double rpab = dot(rab, pab);
179			double rpabsq = rpab * rpab;
180
181			if (rpabsq < (rabsq * -diffsq)){
182			return consFail;
183			}
184
185			double rma = 1.0 / consElem1->getMass();
186			double rmb = 1.0 / consElem2->getMass();
187
188			double gab = diffsq / (2.0 * (rma + rmb) * rpab);
189
190			Vector3d delta = rab * gab;
191
192			//set atom1's position
193			posA += rma * delta;
194			consElem1->setPos(posA);
195
196			//set atom2's position
197			posB -= rmb * delta;
198			consElem2->setPos(posB);
199
200			delta /= dt_;
201
202			//set atom1's velocity
203			Vector3d velA = consElem1->getVel();
204			velA += rma * delta;
205			consElem1->setVel(velA);
206
207			//set atom2's velocity
208			Vector3d velB = consElem2->getVel();
209			velB -= rmb * delta;
210			consElem2->setVel(velB);
211
212			return consSuccess;
213			}
214			else
215			return consAlready;
216
217			}
218
219
220			int Rattle::constraintPairB(ConstraintPair* consPair){
221			ConstraintElem* consElem1 = consPair->getConsElem1();
222			ConstraintElem* consElem2 = consPair->getConsElem2();
223
224
225			Vector3d velA = consElem1->getVel();
226			Vector3d velB = consElem2->getVel();
227
228			Vector3d dv = velA - velB;
229
230			Vector3d posA = consElem1->getPos();
231			Vector3d posB = consElem2->getPos();
232
233			Vector3d rab = posA - posB;
234
235			currentSnapshot_->wrapVector(rab);
236
237			double rma = 1.0 / consElem1->getMass();
238			double rmb = 1.0 / consElem2->getMass();
239
240			double rvab = dot(rab, dv);
241
242			double gab = -rvab / ((rma + rmb) * consPair->getConsDistSquare());
243
244			if (fabs(gab) > consTolerance_){
245			Vector3d delta = rab * gab;
246
247			velA += rma * delta;
248			consElem1->setVel(velA);
249
250			velB -= rmb * delta;
251			consElem2->setVel(velB);
252
253			return consSuccess;
254			}
255			else
256			return consAlready;
257
258			}
259
260			}